Evidence map›Paper›PMID 39966714›Full record

ArticleBMC genomics2025

Insights from draft genomes of Heterodera species isolated from field soil samples.

Akshita Jain, Tongda Li, Daniel C Huston, Jatinder Kaur, Conrad Trollip, John Wainer, Mike Hodda, Katherine Linsell, Ian T Riley, Halil Toktay and 4 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Akshita JainSchool of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia. Akshita.jain@agriculture.vic.gov.au.
Tongda LiCentre for AgriBioscience, Agriculture Victoria Research, Department of Energy, Environment and Climate Action (DEECA), Bundoora, VIC, 3083, Australia.
Daniel C HustonAustralian National Insect Collection, National Research Collection Australia, CSIRO, PO Box 1700, Canberra, ACT, 2601, Australia.
Jatinder KaurSchool of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
Conrad TrollipForest Science, NSW Department of Primary Industries, Parramatta, NSW, 2150, Australia.
John WainerCentre for AgriBioscience, Agriculture Victoria Research, Department of Energy, Environment and Climate Action (DEECA), Bundoora, VIC, 3083, Australia.
Mike HoddaAustralian National Insect Collection, National Research Collection Australia, CSIRO, PO Box 1700, Canberra, ACT, 2601, Australia.
Katherine LinsellSouth Australian Research and Development Institute, Adelaide, SA, 5064, Australia.
Ian T RileySchool of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
Halil ToktayDepartment of Plant Production and Technologies, Faculty of Agricultural Science and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey.
Eniola Ajibola OlowuDepartment of Plant Production and Technologies, Faculty of Agricultural Science and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey.
Jacqueline EdwardsSchool of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
Brendan RodoniSchool of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
Timothy SawbridgeSchool of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe nematode phylum includes many species key to soil food webs with trophic behaviours extending from feeding on microbes to macrofauna and plant roots. Among these, the plant parasitic cyst nematodes retain their eggs in protective cysts prolonging their survival under harsh conditions. These nematodes, including those from the genus Heterodera, cause significant economic losses in agricultural systems. Understanding of nematode diversity and ecology has expanded through application of genomic research, however, for Heterodera species there are very few available whole genome sequences. Sequencing and assembling Heterodera genomes is challenging due to various technical limitations imposed by the biology of Heterodera. Overcoming these limitations is essential for comprehensive insights into Heterodera parasitic interactions with plants, population studies, and for Australian biosecurity implications.

resultsWe hereby present draft genomes of six species of which Heterodera australis, H. humuli, H. mani and H. trifolii are presently recorded in Australia and two species, H. avenae and H. filipjevi, currently absent from Australia. The draft genomes were sequenced from genomic DNA isolated from 50 cysts each using an Illumina NovaSeq short read sequencing platform. The data revealed disparity in sequencing yield between species. What was previously identified as H. avenae in Australia using morphological traits is now confirmed as H. australis and may have consequences for wheat breeding programs in Australia that are breeding for resistance to H. avenae. A multigene phylogeny placed the sequenced species into taxonomic phylogenetic perspective. Genomic comparisons within the Avenae species group revealed orthologous gene clusters within the species, emphasising the shared and unique features of the group. The data also revealed the presence of a Wolbachia species, a putative bacterial endosymbiont from Heterodera humuli short read sequencing data.

conclusionGenomic research holds immense significance for agriculture, for understanding pest species diversity and the development of effective management strategies. This study provides insight into Heterodera, cyst nematode genomics and the associated symbionts and this work will serve as a baseline for further genomic analyses in this economically important nematode group.

Indexed as

Genome, HelminthGenomicsSoilTylenchoideaAnimalsPhylogenySoilAustralian BiosecurityCyst nematodesHeteroderaHeteroderidaeTylenchoideaWhole genome sequencingWolbachia

Identifiers

PMID39966714
PMCPMC11834393

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.